Abstract
The important role of the microbes residing in our gut, collectively called the microbiota, in human health is widely acknowledged. There are numerous factors that have an impact on the microbiota in the gut of which diet is considered a crucial one. In this chapter we highlight our current knowledge on the ecology of the microbiota in adults and how it is affected by diet. We summarize observations from different cross-sectional and intervention studies that focused on the impact of diet on microbiota composition and activity. Special attention is paid to which microbial metabolites can be produced in the gut; how these are affected by different dietary components such as carbohydrates, fat, and proteins; and how these are associated to human health. Finally, we provide recommendations for future intervention studies in order to improve our understanding of the complex interplay between microbes, diet, and ourselves.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Albenberg, L., Esipova, T. V., Judge, C. P., Bittinger, K., Chen, J., Laughlin, A., Grunberg, S., Baldassano, R. N., Lewis, J. D., & Li, H. (2014). Correlation between intraluminal oxygen gradient and radial partitioning of intestinal microbiota. Gastroenterology, 147(5), 1055–1063. e1058.
An, R., Wilms, E., Masclee, A. A., Smidt, H., Zoetendal, E. G., & Jonkers, D. (2018). Age-dependent changes in GI physiology and microbiota: Time to reconsider? Gut, 67(12), 2213–2222.
Arumugam, M., Raes, J., Pelletier, E., Le Paslier, D., Yamada, T., Mende, D. R., Fernandes, G. R., Tap, J., Bruls, T., Batto, J.-M., Bertalan, M., Borruel, N., Casellas, F., Fernandez, L., Gautier, L., Hansen, T., Hattori, M., Hayashi, T., Kleerebezem, M., Kurokawa, K., Leclerc, M., Levenez, F., Manichanh, C., Nielsen, H. B., Nielsen, T., Pons, N., Poulain, J., Qin, J., Sicheritz-Ponten, T., Tims, S., Torrents, D., Ugarte, E., Zoetendal, E. G., Wang, J., Guarner, F., Pedersen, O., de Vos, W. M., Brunak, S., Dore, J., Weissenbach, J., Ehrlich, S. D., Bork, P., & Meta, H. I. T. C. (2011). Enterotypes of the human gut microbiome. Nature, 473(7346), 174–180.
Atuma, C., Strugala, V., Allen, A., & Holm, L. (2001). The adherent gastrointestinal mucus gel layer: Thickness and physical state in vivo. American Journal of Physiology-Gastrointestinal and Liver Physiology, 280(5), G922–G929.
Azcárate-Peril, M. A., Sikes, M., & Bruno-Bárcena, J. M. (2011). The intestinal microbiota, gastrointestinal environment and colorectal cancer: A putative role for probiotics in prevention of colorectal cancer? American Journal of Physiology-Gastrointestinal and Liver Physiology, 301(3), G401–G424.
Bashiardes, S., Godneva, A., Elinav, E., & Segal, E. (2018). Towards utilization of the human genome and microbiome for personalized nutrition. Current Opinion in Biotechnology, 51, 57–63.
Begley, M., Gahan, C. G., & Hill, C. (2005). The interaction between bacteria and bile. FEMS Microbiology Reviews, 29(4), 625–651.
Bonder, M. J., Tigchelaar, E. F., Cai, X., Trynka, G., Cenit, M. C., Hrdlickova, B., Zhong, H., Vatanen, T., Gevers, D., Wijmenga, C., Wang, Y., & Zhernakova, A. (2016). The influence of a short-term gluten-free diet on the human gut microbiome. Genome Medicine, 8(1), 45.
Booijink, C. C., El-Aidy, S., Rajilić-Stojanović, M., Heilig, H. G., Troost, F. J., Smidt, H., Kleerebezem, M., De Vos, W. M., & Zoetendal, E. G. (2010). High temporal and inter-individual variation detected in the human ileal microbiota. Environmental Microbiology, 12(12), 3213–3227.
Bui, T. P. N., Ritari, J., Boeren, S., De Waard, P., Plugge, C. M., & De Vos, W. M. (2015). Production of butyrate from lysine and the Amadori product fructoselysine by a human gut commensal. Nature Communications, 6, 10062.
Canfora, E. E., van der Beek, C. M., Hermes, G. D., Goossens, G. H., Jocken, J. W., Holst, J. J., van Eijk, H. M., Venema, K., Smidt, H., & Zoetendal, E. G. (2017). Supplementation of diet with galacto-oligosaccharides increases bifidobacteria, but not insulin sensitivity, in obese prediabetic individuals. Gastroenterology, 153(1), 87–97.
Carbonero, F., Benefiel, A. C., & Gaskins, H. R. (2012). Contributions of the microbial hydrogen economy to colonic homeostasis. Nature Reviews. Gastroenterology & Hepatology, 9(9), 504–518.
Cheng, J., Ringel-Kulka, T., Heikamp-de Jong, I., Ringel, Y., Carroll, I., De Vos, W. M., Salojärvi, J., & Satokari, R. (2016). Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children. The ISME Journal, 10(4), 1002–1014.
Conlon, M. A., & Bird, A. R. (2014). The impact of diet and lifestyle on gut microbiota and human health. Nutrients, 7(1), 17–44.
Costabile, A., Klinder, A., Fava, F., Napolitano, A., Fogliano, V., Leonard, C., Gibson, G. R., & Tuohy, K. M. (2008). Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: A double-blind, placebo-controlled, crossover study. British Journal of Nutrition, 99(1), 110–120.
Costabile, A., Kolida, S., Klinder, A., Gietl, E., Bäuerlein, M., Frohberg, C., Landschütze, V., & Gibson, G. R. (2010). A double-blind, placebo-controlled, cross-over study to establish the bifidogenic effect of a very-long-chain inulin extracted from globe artichoke (Cynara scolymus) in healthy human subjects. British Journal of Nutrition, 104(7), 1007–1017.
Costea, P. I., Hildebrand, F., Manimozhiyan, A., Bäckhed, F., Blaser, M. J., Bushman, F. D., De Vos, W. M., Ehrlich, S. D., Fraser, C. M., & Hattori, M. (2018). Enterotypes in the landscape of gut microbial community composition. Nature Microbiology, 3(1), 8.
Cummings, J., Pomare, E., Branch, W., Naylor, C., & Macfarlane, G. (1987). Short chain fatty acids in human large intestine, portal, hepatic and venous blood. Gut, 28(10), 1221–1227.
David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., Biddinger, S. B., Dutton, R. J., & Turnbaugh, P. J. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559.
De Filippis, F., Pellegrini, N., Vannini, L., Jeffery, I. B., La Storia, A., Laghi, L., Serrazanetti, D. I., Di Cagno, R., Ferrocino, I., & Lazzi, C. (2016). High-level adherence to a Mediterranean diet beneficially impacts the gut microbiota and associated metabolome. Gut, 65(11), 1812–1821.
De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., Collini, S., Pieraccini, G., & Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences, 107(33), 14691–14696.
De Filippo, C., Di Paola, M., Ramazzotti, M., Albanese, D., Pieraccini, G., Banci, E., Miglietta, F., Cavalieri, D., & Lionetti, P. (2017). Diet, environments, and gut microbiota. a preliminary investigation in children living in rural and urban burkina faso and italy. Frontiers in Microbiology, 8, 1979.
De Palma, G., Nadal, I., Carmen Collado, M., & Sanz, Y. (2009). Effects of a gluten-free diet on gut microbiota and immune function in healthy adult human subjects. British Journal of Nutrition, 102(8), 1154–1160.
de Vos, W. M. (2017). Microbe profile: Akkermansia muciniphila: A conserved intestinal symbiont that acts as the gatekeeper of our mucosa. Microbiology, 163(5), 646–648.
Derrien, M., Vaughan, E. E., Plugge, C. M., & de Vos, W. M. (2004). Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. International Journal of Systematic and Evolutionary Microbiology, 54(5), 1469–1476.
Dewulf, E. M., Cani, P. D., Claus, S. P., Fuentes, S., Puylaert, P. G., Neyrinck, A. M., Bindels, L. B., de Vos, W. M., Gibson, G. R., & Thissen, J.-P. (2013). Insight into the prebiotic concept: Lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut, 62(8), 1112–1121.
Donaldson, G. P., Lee, S. M., & Mazmanian, S. K. (2016). Gut biogeography of the bacterial microbiota. Nature Reviews Microbiology, 14(1), 20–32.
Donia, M. S., & Fischbach, M. A. (2015). Small molecules from the human microbiota. Science, 349(6246), 1254766.
Duncan, S. H., Lobley, G., Holtrop, G., Ince, J., Johnstone, A., Louis, P., & Flint, H. J. (2008). Human colonic microbiota associated with diet, obesity and weight loss. International Journal of Obesity, 32(11), 1720.
Duncan, S. H., Louis, P., Thomson, J. M., & Flint, H. J. (2009). The role of pH in determining the species composition of the human colonic microbiota. Environmental Microbiology, 11(8), 2112–2122.
Elzinga, J., van der Oost, J., de Vos, W. M., & Smidt, H. (2019). The use of defined microbial communities to model host-microbe interactions in the human gut. Microbiology and Molecular Biology Reviews, 83(2), e00054–e00018.
Falony, G., Joossens, M., Vieira-Silva, S., Wang, J., Darzi, Y., Faust, K., Kurilshikov, A., Bonder, M. J., Valles-Colomer, M., & Vandeputte, D. (2016). Population-level analysis of gut microbiome variation. Science, 352(6285), 560–564.
Fava, F., Gitau, R., Griffin, B., Gibson, G., Tuohy, K., & Lovegrove, J. (2013). The type and quantity of dietary fat and carbohydrate alter faecal microbiome and short-chain fatty acid excretion in a metabolic syndrome ‘at-risk’ population. International Journal of Obesity, 37(2), 216.
Feng, Y., Stams, A. J., De Vos, W. M., & Sánchez-Andrea, I. (2017). Enrichment of sulfidogenic bacteria from the human intestinal tract. FEMS Microbiology Letters, 364(4), fnx028.
Foerster, J., Maskarinec, G., Reichardt, N., Tett, A., Narbad, A., Blaut, M., & Boeing, H. (2014). The influence of whole grain products and red meat on intestinal microbiota composition in normal weight adults: A randomized crossover intervention trial. PLoS One, 9(10), e109606.
Frank, D. N., Amand, A. L. S., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007). Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proceedings of the National Academy of Sciences, 104(34), 13780–13785.
Fuentes, S., Rossen, N. G., van der Spek, M. J., Hartman, J. H., Huuskonen, L., Korpela, K., Salojärvi, J., Aalvink, S., de Vos, W. M., & D’Haens, G. R. (2017). Microbial shifts and signatures of long-term remission in ulcerative colitis after faecal microbiota transplantation. The ISME Journal, 11(8), 1877.
Geerlings, S., Kostopoulos, I., de Vos, W., & Belzer, C. (2018). Akkermansia muciniphila in the human gastrointestinal tract: When, where, and how? Microorganisms, 6(3), 75.
Goodrich, J. K., Waters, J. L., Poole, A. C., Sutter, J. L., Koren, O., Blekhman, R., Beaumont, M., Van Treuren, W., Knight, R., & Bell, J. T. (2014). Human genetics shape the gut microbiome. Cell, 159(4), 789–799.
Hald, S., Schioldan, A. G., Moore, M. E., Dige, A., Lærke, H. N., Agnholt, J., Knudsen, K. E. B., Hermansen, K., Marco, M. L., & Gregersen, S. (2016). Effects of arabinoxylan and resistant starch on intestinal microbiota and short-chain fatty acids in subjects with metabolic syndrome: A randomised crossover study. PLoS One, 11(7), e0159223.
Halmos, E. P., Christophersen, C. T., Bird, A. R., Shepherd, S. J., Gibson, P. R., & Muir, J. G. (2014a). Diets that differ in their FODMAP content alter the colonic luminal microenvironment. Gut, 64(1), 93–100.
Halmos, E. P., Power, V. A., Shepherd, S. J., Gibson, P. R., & Muir, J. G. (2014b). A diet low in FODMAPs reduces symptoms of irritable bowel syndrome. Gastroenterology, 146(1), 67–75. e65.
Henning, S. M., Yang, J., Shao, P., Lee, R.-P., Huang, J., Ly, A., Hsu, M., Lu, Q.-Y., Thames, G., & Heber, D. (2017). Health benefit of vegetable/fruit juice-based diet: Role of microbiome. Scientific Reports, 7(1), 2167.
Hermes, G. (2016). Mining the human intestinal microbiota for biomarkers associated with metabolic disorders. Ph.D. thesis, Wageningen University.
Islam, K. S., Fukiya, S., Hagio, M., Fujii, N., Ishizuka, S., Ooka, T., Ogura, Y., Hayashi, T., & Yokota, A. (2011). Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology, 141(5), 1773–1781.
Jantchou, P., Morois, S., Clavel-Chapelon, F., Boutron-Ruault, M.-C., & Carbonnel, F. (2010). Animal protein intake and risk of inflammatory bowel disease: The E3N prospective study. The American Journal of Gastroenterology, 105(10), 2195.
Jones, B. V., Begley, M., Hill, C., Gahan, C. G., & Marchesi, J. R. (2008). Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proceedings of the National Academy of Sciences, 105(36), 13580–13585.
Jones, R. B., Zhu, X. Z., Moan, E., Murff, H. J., Ness, R. M., Seidner, D. L., Sun, S., Yu, C., Dai, Q., Fodor, A. A., Azcarate-Peril, M. A., & Shrubsole, M. J. (2018). Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples. Scientific Reports, 8(1), 4139.
Kashyap, P. C., Marcobal, A., Ursell, L. K., Larauche, M., Duboc, H., Earle, K. A., Sonnenburg, E. D., Ferreyra, J. A., Higginbottom, S. K., & Million, M. (2013). Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology, 144(5), 967–977.
Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011). Human nutrition, the gut microbiome and the immune system. Nature, 474(7351), 327–336.
Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & Bäckhed, F. (2016). From dietary fiber to host physiology: Short-chain fatty acids as key bacterial metabolites. Cell, 165(6), 1332–1345.
Korpela, K., Flint, H. J., Johnstone, A. M., Lappi, J., Poutanen, K., Dewulf, E., Delzenne, N., De Vos, W. M., & Salonen, A. (2014). Gut microbiota signatures predict host and microbiota responses to dietary interventions in obese individuals. PLoS One, 9(3), e90702.
Kovatcheva-Datchary, P., Nilsson, A., Akrami, R., Lee, Y. S., De Vadder, F., Arora, T., Hallen, A., Martens, E., Bjorck, I., & Backhed, F. (2015). Dietary fiber-induced improvement in glucose metabolism is associated with increased abundance of Prevotella. Cell Metabolism, 22(6), 971–982.
Lahti, L., Salojärvi, J., Salonen, A., Scheffer, M., & De Vos, W. M. (2014). Tipping elements in the human intestinal ecosystem. Nature Communications, 5, 4344.
Lappi, J., Salojärvi, J., Kolehmainen, M., Mykkänen, H., Poutanen, K., de Vos, W. M., & Salonen, A. (2013). Intake of whole-grain and fiber-rich rye bread versus refined wheat bread does not differentiate intestinal microbiota composition in Finnish adults with metabolic syndrome. The Journal of Nutrition, 143(5), 648–655.
Larsen, N., Vogensen, F. K., van den Berg, F. W., Nielsen, D. S., Andreasen, A. S., Pedersen, B. K., Al-Soud, W. A., Sørensen, S. J., Hansen, L. H., & Jakobsen, M. (2010). Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One, 5(2), e9085.
Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., & Kennedy, S. (2013). Richness of human gut microbiome correlates with metabolic markers. Nature, 500(7464), 541.
Lepage, P., Seksik, P., Sutren, M., de la Cochetiere, M.-F., Jian, R., Marteau, P., & Doré, J. (2005). Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflammatory Bowel Diseases, 11(5), 473–480.
Levitt, M. D., Furne, J. K., Kuskowski, M., & Ruddy, J. (2006). Stability of human methanogenic flora over 35 years and a review of insights obtained from breath methane measurements. Clinical Gastroenterology and Hepatology, 4(2), 123–129.
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006). Microbial ecology: Human gut microbes associated with obesity. Nature, 444(7122), 1022–1023.
Li, J., Jia, H., Cai, X., Zhong, H., Feng, Q., Sunagawa, S., Arumugam, M., Kultima, J. R., Prifti, E., & Nielsen, T. (2014). An integrated catalog of reference genes in the human gut microbiome. Nature Biotechnology, 32(8), 834.
Lin, S. H., Chou, L. M., Chien, Y. W., Chang, J. S., & Lin, C. I. (2016). Prebiotic effects of xylooligosaccharides on the improvement of microbiota balance in human subjects. Gastroenterology Research and Practice, 2016(2016), 5789232.
Liu, F., Li, P., Chen, M., Luo, Y., Prabhakar, M., Zheng, H., He, Y., Qi, Q., Long, H., & Zhang, Y. (2017). Fructooligosaccharide (FOS) and galactooligosaccharide (GOS) increase bifidobacterium but reduce butyrate producing bacteria with adverse glycemic metabolism in healthy young population. Scientific Reports, 7(1), 11789.
Louis, P., Hold, G. L., & Flint, H. J. (2014). The gut microbiota, bacterial metabolites and colorectal cancer. Nature Reviews Microbiology, 12(10), 661.
Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K., & Knight, R. (2012). Diversity, stability and resilience of the human gut microbiota. Nature, 489(7415), 220–230.
Lynch, S. V., & Pedersen, O. (2016). The human intestinal microbiome in health and disease. New England Journal of Medicine, 375(24), 2369–2379.
Macfarlane, G., Cummings, J., & Allison, C. (1986). Protein degradation by human intestinal bacteria. Microbiology, 132(6), 1647–1656.
Martinez, I., Lattimer, J. M., Hubach, K. L., Case, J. A., Yang, J., Weber, C. G., Louk, J. A., Rose, D. J., Kyureghian, G., Peterson, D. A., Haub, M. D., & Walter, J. (2013). Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME Journal, 7(2), 269–280.
Maslowski, K. M., & Mackay, C. R. (2011). Diet, gut microbiota and immune responses. Nature Immunology, 12(1), 5–9.
Menni, C., Lin, C., Cecelja, M., Mangino, M., Matey-Hernandez, M. L., Keehn, L., Mohney, R. P., Steves, C. J., Spector, T. D., Kuo, C.-F., Chowienczyk, P., & Valdes, A. M. (2018). Gut microbial diversity is associated with lower arterial stiffness in women. European Heart Journal, 39(25), 2390–2397.
Miller, T. L., & Wolin, M. J. (1996). Pathways of acetate, propionate, and butyrate formation by the human fecal microbial flora. Applied and Environmental Microbiology, 62(5), 1589–1592.
Moayyedi, P., Surette, M. G., Kim, P. T., Libertucci, J., Wolfe, M., Onischi, C., Armstrong, D., Marshall, J. K., Kassam, Z., & Reinisch, W. (2015). Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology, 149(1), 102–109. e106.
Nakamura, N., Lin, H. C., McSweeney, C. S., Mackie, R. I., & Gaskins, H. R. (2010). Mechanisms of microbial hydrogen disposal in the human colon and implications for health and disease. Annual Review of Food Science and Technology, 1, 363–395.
Nicholson, J. K., Holmes, E., Kinross, J., Burcelin, R., Gibson, G., Jia, W., & Pettersson, S. (2012). Host-gut microbiota metabolic interactions. Science, 336(6086), 1262–1267.
Nyangale, E. P., Mottram, D. S., & Gibson, G. R. (2012). Gut microbial activity, implications for health and disease: The potential role of metabolite analysis. Journal of Proteome Research, 11(12), 5573–5585.
O’Keefe, S. J., Li, J. V., Lahti, L., Ou, J., Carbonero, F., Mohammed, K., Posma, J. M., Kinross, J., Wahl, E., & Ruder, E. (2015). Fat, fibre and cancer risk in African Americans and rural Africans. Nature Communications, 6, 6342.
O’Toole, P. W., & Jeffery, I. B. (2015). Gut microbiota and aging. Science, 350(6265), 1214–1215.
Ott, B., Skurk, T., Lagkouvardos, L., Fischer, S., Büttner, J., Lichtenegger, M., Clavel, T., Lechner, A., Rychlik, M., & Haller, D. (2018). Short-term overfeeding with dairy cream does not modify gut permeability, the fecal microbiota, or glucose metabolism in young healthy men. The Journal of Nutrition, 148(1), 77–85.
Ou, G., Hedberg, M., Hörstedt, P., Baranov, V., Forsberg, G., Drobni, M., Sandström, O., Wai, S. N., Johansson, I., & Hammarström, M.-L. (2009). Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease. The American Journal of Gastroenterology, 104, 3058–3067.
Ou, J., DeLany, J. P., Zhang, M., Sharma, S., & O’Keefe, S. J. (2012). Association between low colonic short-chain fatty acids and high bile acids in high colon cancer risk populations. Nutrition and Cancer, 64(1), 34–40.
Ou, J., Carbonero, F., Zoetendal, E. G., DeLany, J. P., Wang, M., Newton, K., Gaskins, H. R., & O’keefe, S. J. (2013). Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. The American Journal of Clinical Nutrition, 98(1), 111–120.
Pochart, P., Dore, J., Lemann, F., Goderel, I., & Rambaud, J. C. (1992). Interrelations between populations of methanogenic archaea and sulfate-reducing bacteria in the human colon. FEMS Microbiology Letters, 98(1–3), 225–228.
Qin, J. J., Li, R. Q., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., Mende, D. R., Li, J. H., Xu, J. M., Li, S. C., Li, D. F., Cao, J. J., Wang, B., Liang, H. Q., Zheng, H. S., Xie, Y. L., Tap, J., Lepage, P., Bertalan, M., Batto, J. M., Hansen, T., Le Paslier, D., Linneberg, A., Nielsen, H. B., Pelletier, E., Renault, P., Sicheritz-Ponten, T., Turner, K., Zhu, H. M., Yu, C., Li, S. T., Jian, M., Zhou, Y., Li, Y. R., Zhang, X. Q., Li, S. G., Qin, N., Yang, H. M., Wang, J., Brunak, S., Dore, J., Guarner, F., Kristiansen, K., Pedersen, O., Parkhill, J., Weissenbach, J., Bork, P., Ehrlich, S. D., Wang, J., & Consortium, M. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59–U70.
Rajilić-Stojanović, M., Smidt, H., & De Vos, W. M. (2007). Diversity of the human gastrointestinal tract microbiota revisited. Environmental Microbiology, 9(9), 2125–2136.
Rajilić-Stojanović, M., Heilig, H. G., Tims, S., Zoetendal, E. G., & Vos, W. M. (2013). Long-term monitoring of the human intestinal microbiota composition. Environmental Microbiology, 15(4), 1146–1159.
Reiss, A., Jacobi, M., Rusch, K., & Schwiertz, A. (2016). Association of dietary type with fecal microbiota and short chain fatty acids in vegans and omnivores. The Journal International Society of Microbiota, 2, 1.
Rey, F. E., Faith, J. J., Bain, J., Muehlbauer, M. J., Stevens, R. D., Newgard, C. B., & Gordon, J. I. (2010). Dissecting the in vivo metabolic potential of two human gut acetogens. Journal of Biological Chemistry, 285(29), 22082–22090.
Ridlon, J. M., Kang, D.-J., & Hylemon, P. B. (2006). Bile salt biotransformations by human intestinal bacteria. Journal of Lipid Research, 47(2), 241–259.
Ridlon, J. M., Kang, D. J., Hylemon, P. B., & Bajaj, J. S. (2014). Bile acids and the gut microbiome. Current Opinion in Gastroenterology, 30(3), 332.
Roager, H. M., Vogt, J. K., Kristensen, M., Hansen, L. B. S., Ibrügger, S., Mærkedahl, R. B., Bahl, M. I., Lind, M. V., Nielsen, R. L., & Frøkiær, H. (2017). Whole grain-rich diet reduces body weight and systemic low-grade inflammation without inducing major changes of the gut microbiome: A randomised cross-over trial. Gut, 68(1), 83–93.
Ross, A. B., Bruce, S. J., Blondel-Lubrano, A., Oguey-Araymon, S., Beaumont, M., Bourgeois, A., Nielsen-Moennoz, C., Vigo, M., Fay, L.-B., & Kochhar, S. (2011). A whole-grain cereal-rich diet increases plasma betaine, and tends to decrease total and LDL-cholesterol compared with a refined-grain diet in healthy subjects. British Journal of Nutrition, 105(10), 1492–1502.
Rossen, N. G., Fuentes, S., van der Spek, M. J., Tijssen, J. G., Hartman, J. H., Duflou, A., Löwenberg, M., van den Brink, G. R., Mathus-Vliegen, E. M., & de Vos, W. M. (2015). Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology, 149(1), 110–118. e114.
Russell, W. R., Gratz, S. W., Duncan, S. H., Holtrop, G., Ince, J., Scobbie, L., Duncan, G., Johnstone, A. M., Lobley, G. E., & Wallace, R. J. (2011). High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. The American Journal of Clinical Nutrition, 93(5), 1062–1072.
Salonen, A., Lahti, L., Salojarvi, J., Holtrop, G., Korpela, K., Duncan, S. H., Date, P., Farquharson, F., Johnstone, A. M., Lobley, G. E., Louis, P., Flint, H. J., & de Vos, W. M. (2014). Impact of diet and individual variation on intestinal microbiota composition and fermentation products in obese men. ISME Journal, 8(11), 2218–2230.
Saresella, M., Mendozzi, L., Rossi, V., Mazzali, F., Piancone, F., LaRosa, F., Marventano, I., Caputo, D., Felis, G. E., & Clerici, M. (2017). Immunological and clinical effect of diet modulation of the gut microbiome in multiple sclerosis patients: A pilot study. Frontiers in Immunology, 8, 1391.
Schwiertz, A., Taras, D., Schaefer, K., Beijer, S., Bos, N. A., Donus, C., & Hardt, P. D. (2010). Microbiota and SCFA in lean and overweight healthy subjects. Obesity, 18(1), 190–195.
Segal, I., Walker, A., Lord, S., & Cummings, J. (1988). Breath methane and large bowel cancer risk in contrasting African populations. Gut, 29(5), 608–613.
Sender, R., Fuchs, S., & Milo, R. (2016a). Are we really vastly outnumbered? Revisiting the ratio of bacterial to host cells in humans. Cell, 164(3), 337–340.
Sender, R., Fuchs, S., & Milo, R. (2016b). Revised estimates for the number of human and bacteria cells in the body. PLoS Biology, 14(8), e1002533.
Shetty, S. A., Hugenholtz, F., Lahti, L., Smidt, H., & de Vos, W. M. (2017). Intestinal microbiome landscaping: Insight in community assemblage and implications for microbial modulation strategies. FEMS Microbiology Reviews, 41(2), 182–199.
Shetty, S. A., Smidt, H., & de Vos, W. M. (2019). Reconstructing functional networks in the human intestinal tract using synthetic microbiomes. Current Opinion in Biotechnology, 58, 146–154.
Shoaie, S., Ghaffari, P., Kovatcheva-Datchary, P., Mardinoglu, A., Sen, P., Pujos-Guillot, E., de Wouters, T., Juste, C., Rizkalla, S., & Chilloux, J. (2015). Quantifying diet-induced metabolic changes of the human gut microbiome. Cell Metabolism, 22(2), 320–331.
Sonnenburg, E. D., Smits, S. A., Tikhonov, M., Higginbottom, S. K., Wingreen, N. S., & Sonnenburg, J. L. (2016). Diet-induced extinctions in the gut microbiota compound over generations. Nature, 529(7585), 212–U208.
Stams, A. J., & Plugge, C. M. (2009). Electron transfer in syntrophic communities of anaerobic bacteria and archaea. Nature Reviews Microbiology, 7(8), 568.
Staudacher, H. M., Lomer, M. C., Anderson, J. L., Barrett, J. S., Muir, J. G., Irving, P. M., & Whelan, K. (2012). Fermentable carbohydrate restriction reduces luminal bifidobacteria and gastrointestinal symptoms in patients with irritable bowel syndrome. The Journal of Nutrition, 142(8), 1510–1518.
Tap, J., Furet, J. P., Bensaada, M., Philippe, C., Roth, H., Rabot, S., Lakhdari, O., Lombard, V., Henrissat, B., & Corthier, G. (2015). Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults. Environmental Microbiology, 17(12), 4954–4964.
The Human Microbiome Project Consortium. (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207–214.
Tuohy, K., Kolida, S., Lustenberger, A., & Gibson, G. R. (2001). The prebiotic effects of biscuits containing partially hydrolysed guar gum and fructo-oligosaccharides—A human volunteer study. British Journal of Nutrition, 86(3), 341–348.
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature, 444(7122), 1027–1031.
Van Nood, E., Vrieze, A., Nieuwdorp, M., Fuentes, S., Zoetendal, E. G., de Vos, W. M., Visser, C. E., Kuijper, E. J., Bartelsman, J. F., & Tijssen, J. G. (2013). Duodenal infusion of donor feces for recurrent Clostridium difficile. New England Journal of Medicine, 368(5), 407–415.
Vandeputte, D., Falony, G., Vieira-Silva, S., Wang, J., Sailer, M., Theis, S., Verbeke, K., & Raes, J. (2017). Prebiotic inulin-type fructans induce specific changes in the human gut microbiota. Gut, 66(11), 1968–1974.
Vermeire, S., Joossens, M., Verbeke, K., Wang, J., Machiels, K., Sabino, J., Ferrante, M., Van Assche, G., Rutgeerts, P., & Raes, J. (2016). Donor species richness determines faecal microbiota transplantation success in inflammatory bowel disease. Journal of Crohn’s and Colitis, 10(4), 387–394.
Vital, M., Howe, A. C., & Tiedje, J. M. (2014). Revealing the bacterial butyrate synthesis pathways by analyzing (meta) genomic data. MBio, 5(2), e00889–e00814.
Vuholm, S., Nielsen, D. S., Iversen, K. N., Suhr, J., Westermann, P., Krych, L., Andersen, J. R., & Kristensen, M. (2017). Whole-grain rye and wheat affect some markers of gut health without altering the fecal microbiota in healthy overweight adults: A 6-week randomized trial. The Journal of Nutrition, 147(11), 2067–2075.
Walker, A. W., Ince, J., Duncan, S. H., Webster, L. M., Holtrop, G., Ze, X., Brown, D., Stares, M. D., Scott, P., & Bergerat, A. (2011). Dominant and diet-responsive groups of bacteria within the human colonic microbiota. The ISME Journal, 5(2), 220–230.
Wang, T., Cai, G., Qiu, Y., Fei, N., Zhang, M., Pang, X., Jia, W., Cai, S., & Zhao, L. (2012). Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. The ISME Journal, 6(2), 320–329.
Windey, K., De Preter, V., Louat, T., Schuit, F., Herman, J., Vansant, G., & Verbeke, K. (2012a). Modulation of protein fermentation does not affect fecal water toxicity: A randomized cross-over study in healthy subjects. PLoS One, 7(12), e52387.
Windey, K., De Preter, V., & Verbeke, K. (2012b). Relevance of protein fermentation to gut health. Molecular Nutrition & Food Research, 56(1), 184–196.
Wu, G. D., Chen, J., Hoffmann, C., Bittinger, K., Chen, Y.-Y., Keilbaugh, S. A., Bewtra, M., Knights, D., Walters, W. A., & Knight, R. (2011). Linking long-term dietary patterns with gut microbial enterotypes. Science, 334(6052), 105–108.
Xiao, S., Fei, N., Pang, X., Shen, J., Wang, L., Zhang, B., Zhang, M., Zhang, X., Zhang, C., & Li, M. (2014). A gut microbiota-targeted dietary intervention for amelioration of chronic inflammation underlying metabolic syndrome. FEMS Microbiology Ecology, 87(2), 357–367.
Yatsunenko, T., Rey, F. E., Manary, M. J., Trehan, I., Dominguez-Bello, M. G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R. N., Anokhin, A. P., Heath, A. C., Warner, B., Reeder, J., Kuczynski, J., Caporaso, J. G., Lozupone, C. A., Lauber, C., Clemente, J. C., Knights, D., Knight, R., & Gordon, J. I. (2012). Human gut microbiome viewed across age and geography. Nature, 486(7402), 222.
Zeevi, D., Korem, T., Zmora, N., Israeli, D., Rothschild, D., Weinberger, A., Ben-Yacov, O., Lador, D., Avnit-Sagi, T., Lotan-Pompan, M., Suez, J., Mahdi, J. A., Matot, E., Malka, G., Kosower, N., Rein, M., Zilberman-Schapira, G., Dohnalova, L., Pevsner-Fischer, M., Bikovsky, R., Halpern, Z., Elinav, E., & Segal, E. (2015). Personalized nutrition by prediction of glycemic responses. Cell, 163(5), 1079–1094.
Zhernakova, A., Kurilshikov, A., Bonder, M. J., Tigchelaar, E. F., Schirmer, M., Vatanen, T., Mujagic, Z., Vila, A. V., Falony, G., & Vieira-Silva, S. (2016). Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity. Science, 352(6285), 565–569.
Zoetendal, E. G., & de Vos, W. M. (2014). Effect of diet on the intestinal microbiota and its activity. Current Opinion in Gastroenterology, 30(2), 189–195.
Zoetendal, E. G., von Wright, A., Vilpponen-Salmela, T., Ben-Amor, K., Akkermans, A. D., & de Vos, W. M. (2002). Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Applied and Environmental Microbiology, 68(7), 3401–3407.
Zoetendal, E. G., Raes, J., Van Den Bogert, B., Arumugam, M., Booijink, C. C., Troost, F. J., Bork, P., Wels, M., De Vos, W. M., & Kleerebezem, M. (2012). The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. The ISME Journal, 6(7), 1415–1426.
Acknowledgements
The research by Taojun Wang is financially supported by the China Scholarship Council (File No. 201600090211).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Wang, T., Roest, D.I.M., Smidt, H., Zoetendal, E.G. (2019). “We Are What We Eat”: How Diet Impacts the Gut Microbiota in Adulthood. In: Azcarate-Peril, M., Arnold, R., Bruno-Bárcena, J. (eds) How Fermented Foods Feed a Healthy Gut Microbiota. Springer, Cham. https://doi.org/10.1007/978-3-030-28737-5_11
Download citation
DOI: https://doi.org/10.1007/978-3-030-28737-5_11
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-28736-8
Online ISBN: 978-3-030-28737-5
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)